Entering edit mode
Oleg Sklyar
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260
@oleg-sklyar-1882
Last seen 10.2 years ago
Hi,
I am having troubles with cateGOry as follows:
> m <- cateGOry(go$refseq_dna, go$go, FALSE)
Error in augmentByAncestors(ux) : GO terms 24, 172, 1978, 1979, 4442
were mentioned in 'x' but were not found in the GO package.
what this error means was not clear, so I tried those as indexes in my
data, as follows first, or as GO ids as follows second. Neither
worked.
Any idea? Thanks, Oleg
> index <- c(24, 172, 1978, 1979, 4441)
> m <- cateGOry(go$refseq_dna[-index], go$go[-index], FALSE)
Error in augmentByAncestors(ux) : GO terms 24, 172, 1978, 1979, 4442
were mentioned in 'x' but were not found in the GO package.
> terms <- c("GO:0000024", "GO:0000172", "GO:0001978", "GO:0001979",
"GO:0004442")
> index <- which(go$go %in% terms)
> go$go[index]
[1] "GO:0000172" "GO:0000172"
> m <- cateGOry(go$refseq_dna[-index], go$go[-index], FALSE)
Error in augmentByAncestors(ux) : GO terms 24, 172, 1978, 1979, 4441
were mentioned in 'x' but were not found in the GO package.
--
Dr Oleg Sklyar | EBI-EMBL, Cambridge CB10 1SD, UK | +44-1223-494466